Management of complex perianal fistulas remains a challenge as aconsequence of the serious limitations of currently available treatmentsregarding the problems of faecal incontinence, Mesenchymal adult stemcells extracted from certain tissues, such as bone marrow, candifferentiate into various cell types. Therefore, we have tried to use suchcells to stimulate healing in complex and recurrent anal fistulae.We designed a clinical trial, involving 15 patients with complex andrecurrent anal fistulae, to test the feasibility and safety of autologous stemcells transplantation in the treatment of fistulae, with evaluation for sixmonths regarding short term post operative complications, healing rateand complete closure of the external opening.In this study we noticed during the follow up period that the healedfistulas were noticed in 8 patients (53.3%) and the mean period of healingwas noticed in 97.5 days (3- 4 months post injection) , there were twosubgroups of non healing fistulas either incomplete healing which wasnoticed in 4 patients (26.7%) who reported better quality of life and noother intervention was needed (except for one case) and in the other subgroup 3 patients (20%) had no change in the pre and post injectionsymptoms regarding the continuous discharge (begin serous then turn intopurulent discharge) and were confirmed non healed by means ofradiological assessments.The use of Autologous Stem cells in the treatment of the anal fistula is arecent technique. Despite the rate of failure or incomplete healing but itstill provides a solution for the avoidance of continence impairment andextensive tissue scaring which follows the ordinary surgical procedures.